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- PDB-5ctm: Structure of BPu1 beta-lactamase -

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Basic information

Entry
Database: PDB / ID: 5ctm
TitleStructure of BPu1 beta-lactamase
ComponentsBeta-lactamase
KeywordsHYDROLASE / beta-lactamase
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic / plasma membrane
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / DI(HYDROXYETHYL)ETHER / Beta-lactamase
Similarity search - Component
Biological speciesBacillus pumilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1 Å
AuthorsSmith, C.A. / Vakulenko, S.B.
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Class D beta-lactamases do exist in Gram-positive bacteria.
Authors: Toth, M. / Antunes, N.T. / Stewart, N.K. / Frase, H. / Bhattacharya, M. / Smith, C.A. / Vakulenko, S.B.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-lactamase
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4808
Polymers54,6822
Non-polymers7986
Water12,052669
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8435
Polymers27,3411
Non-polymers5024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6363
Polymers27,3411
Non-polymers2952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.660, 79.870, 65.010
Angle α, β, γ (deg.)90.000, 92.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Beta-lactamase


Mass: 27341.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus pumilus (bacteria) / Gene: BPUM_2340 / Production host: Escherichia coli (E. coli) / References: UniProt: A8FFI9, beta-lactamase
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 2% Tacsimate (pH 5.0), 0.1 M sodium citrate pH 5.6, 16% PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1→64.9 Å / Num. obs: 261147 / % possible obs: 99.9 % / Redundancy: 6.4 % / Net I/σ(I): 10.5
Reflection shellResolution: 1→1.04 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1→37.696 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1383 13117 5.02 %
Rwork0.1259 247974 -
obs0.1265 261091 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 44.46 Å2 / Biso mean: 17.5944 Å2 / Biso min: 6.45 Å2
Refinement stepCycle: final / Resolution: 1→37.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3841 0 91 692 4624
Biso mean--25.21 27.51 -
Num. residues----465
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084351
X-RAY DIFFRACTIONf_angle_d1.4065926
X-RAY DIFFRACTIONf_chiral_restr0.128610
X-RAY DIFFRACTIONf_plane_restr0.008761
X-RAY DIFFRACTIONf_dihedral_angle_d15.0581714
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1-1.01140.2334270.218682508677
1.0114-1.02330.21244460.205581678613
1.0233-1.03570.20154470.18782778724
1.0357-1.04890.1744280.16882518679
1.0489-1.06270.16374500.154182138663
1.0627-1.07720.15374440.144681978641
1.0772-1.09260.14714160.136482868702
1.0926-1.10890.13454270.126882978724
1.1089-1.12620.13794370.119381848621
1.1262-1.14470.12634290.11682838712
1.1447-1.16450.1224410.11582708711
1.1645-1.18560.12464420.112782018643
1.1856-1.20840.14734310.11582878718
1.2084-1.23310.11924330.109482128645
1.2331-1.25990.11774400.106683008740
1.2599-1.28920.12214470.102182648711
1.2892-1.32150.12524140.102982848698
1.3215-1.35720.11214510.100982128663
1.3572-1.39710.11814560.103982598715
1.3971-1.44220.12554250.105782758700
1.4422-1.49380.11844740.10182498723
1.4938-1.55360.12064330.101682878720
1.5536-1.62430.11213950.10482658660
1.6243-1.70990.12134130.106983548767
1.7099-1.81710.13394570.116882358692
1.8171-1.95740.13894330.12182628695
1.9574-2.15430.13233980.123183678765
2.1543-2.4660.13874530.13282498702
2.466-3.10670.15364700.145283408810
3.1067-37.72310.14854600.137883978857

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